Quickstart

Installation

SASS is both a standalone application and a Fiji plugin.

Standalone

  1. Download the latest .jar file from the SASS releases page.
  2. You will also need to download the latest ALICA_ACPack .jar, which contains the run-time components for control systems simulations.
  3. Place both .jars in the folder of your choosing.

Fiji

  1. Download the latest .jar file from the SASS releases page.
  2. You will also need to download the latest ALICA_ACPack .jar, which contains the run-time components for control systems simulations.
  3. Copy the SASS .jar file into your ~/Fiji.app/plugins/ folder, where Fiji.app is root directory for your Fiji installation.
  4. Copy the ALICA_ACPack .jar file into your ~/Fiji.app/jars folder.
  5. Restart Fiji.

You should now see SASS appear as a menu item in the the Plugins menu.

Run a simulation

Standalone

Before starting, make sure that you have a copy of the file example_random_2d_fluorophores.bsh from the SASS respository’s scripts folder. When using SASS in standalone mode, it is most commonly used as a command line application.

  1. From the command line, navigate to the folder where you placed the SASS .jar file that you downloaded in the installation step.
  2. Enter the command java -jar SASS_-<VERSION>.jar -s example_random_2d_fluorophores.bsh.
  3. If you want to save the simulation’s output, ensure that any call to the saveStack(…) method is uncommented inside the script and rerun the simulation.

Fiji

  1. Launch Fiji. (If you’re launch Fiji from the command line, ensure that you are first in the Fiji root directory.)
  2. Navigate to Plugins > SASS > Simulator.
  3. Ensure that Manual is selected in the Controller drop-down box.
  4. Click the Initialize button.
  5. Rearrange the windows so that you can find the dialog with the controller set point and the Start and Stop buttons.
  6. Click Start to start the simulation. You should see images begin streaming into the simulation’s image stack.
  7. Click the Stop button to pause the simulation.
  8. Change the Controller setpoint value and click Start again to resume the simulation with a new laser power.